Incidental Mutation 'R1715:Rfx4'
ID 190946
Institutional Source Beutler Lab
Gene Symbol Rfx4
Ensembl Gene ENSMUSG00000020037
Gene Name regulatory factor X, 4 (influences HLA class II expression)
Synonyms 4933412G19Rik
MMRRC Submission 039748-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1715 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 84591926-84742402 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 84680144 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 107 (N107S)
Ref Sequence ENSEMBL: ENSMUSP00000128690 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000060397] [ENSMUST00000095388] [ENSMUST00000166696]
AlphaFold Q7TNK1
Predicted Effect noncoding transcript
Transcript: ENSMUST00000020226
Predicted Effect probably damaging
Transcript: ENSMUST00000060397
AA Change: N250S

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000051107
Gene: ENSMUSG00000020037
AA Change: N250S

DomainStartEndE-ValueType
Pfam:RFX_DNA_binding 58 136 7.9e-37 PFAM
Blast:HisKA 293 356 5e-7 BLAST
low complexity region 503 515 N/A INTRINSIC
low complexity region 521 537 N/A INTRINSIC
low complexity region 599 611 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000095388
AA Change: N156S

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000093035
Gene: ENSMUSG00000020037
AA Change: N156S

DomainStartEndE-ValueType
SCOP:d1kwha_ 11 201 6e-3 SMART
Blast:HisKA 199 262 4e-7 BLAST
low complexity region 409 421 N/A INTRINSIC
low complexity region 427 443 N/A INTRINSIC
low complexity region 505 517 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000166696
AA Change: N107S

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000128690
Gene: ENSMUSG00000020037
AA Change: N107S

DomainStartEndE-ValueType
Blast:HisKA 150 213 6e-7 BLAST
low complexity region 360 372 N/A INTRINSIC
low complexity region 378 394 N/A INTRINSIC
low complexity region 456 468 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 94.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
PHENOTYPE: Inactivating null allele or homozygous point mutation alleles exhibit missing dorsal midline structure of the cortex including the subcommissural organ and neonatal lethality. Heterozygous null mice have congenital hydrocephalus. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8a G A 11: 109,982,406 (GRCm39) T12M probably damaging Het
Alms1 T A 6: 85,606,034 (GRCm39) Y2561* probably null Het
Atp10a G A 7: 58,436,253 (GRCm39) V348I probably damaging Het
Best2 T C 8: 85,737,852 (GRCm39) Y181C probably benign Het
Btaf1 T A 19: 36,946,521 (GRCm39) D442E probably damaging Het
Carmil3 T G 14: 55,741,989 (GRCm39) V1153G probably benign Het
Cc2d2a A G 5: 43,876,003 (GRCm39) I993M probably damaging Het
Ccng1 G A 11: 40,642,941 (GRCm39) P169S probably benign Het
Cip2a C T 16: 48,826,082 (GRCm39) T383I probably benign Het
Cmtr2 T C 8: 110,949,430 (GRCm39) L580P probably damaging Het
Col22a1 T C 15: 71,878,830 (GRCm39) E109G possibly damaging Het
Cplane1 T A 15: 8,256,384 (GRCm39) probably null Het
Crispld2 G T 8: 120,750,388 (GRCm39) W264L possibly damaging Het
Cyp2c38 T C 19: 39,393,239 (GRCm39) H276R probably benign Het
Dag1 A T 9: 108,085,914 (GRCm39) V409E possibly damaging Het
Efcab15 T C 11: 103,090,650 (GRCm39) probably null Het
Emc8 T C 8: 121,385,294 (GRCm39) N146S probably benign Het
Glt8d1 T C 14: 30,733,478 (GRCm39) V321A possibly damaging Het
Gm5174 C T 10: 86,492,776 (GRCm39) noncoding transcript Het
Hdac10 G T 15: 89,010,912 (GRCm39) probably null Het
Hectd4 A G 5: 121,482,881 (GRCm39) D3144G possibly damaging Het
Ifna11 C T 4: 88,738,473 (GRCm39) S93L probably damaging Het
Il16 T C 7: 83,297,936 (GRCm39) N431S probably benign Het
Irf8 A T 8: 121,481,127 (GRCm39) E237V probably damaging Het
Lrp1b A G 2: 41,075,993 (GRCm39) Y1769H probably damaging Het
Lrrc9 A G 12: 72,524,073 (GRCm39) N761D probably damaging Het
Mbtps1 T C 8: 120,269,469 (GRCm39) Y207C probably benign Het
Myo9a A G 9: 59,739,583 (GRCm39) E765G probably damaging Het
Nlrp3 A G 11: 59,434,177 (GRCm39) D80G probably damaging Het
Or12k8 G A 2: 36,975,188 (GRCm39) P191S probably damaging Het
Or2ag15 G C 7: 106,340,755 (GRCm39) P129A probably damaging Het
Or7g18 A T 9: 18,787,090 (GRCm39) I156F probably benign Het
Pcyt2 T A 11: 120,506,677 (GRCm39) probably null Het
Plxnd1 T C 6: 115,945,642 (GRCm39) T944A probably benign Het
Prss3b A G 6: 41,009,870 (GRCm39) probably null Het
Psd4 A T 2: 24,295,344 (GRCm39) I833F probably damaging Het
Psmd7 A G 8: 108,307,817 (GRCm39) I222T probably benign Het
Rap2b A G 3: 61,272,611 (GRCm39) E45G probably damaging Het
Rbm22 T C 18: 60,693,916 (GRCm39) S7P possibly damaging Het
Rbpms2 ACTGCTGCTGCTGCTGC ACTGCTGCTGCTGCTGCTGC 9: 65,558,948 (GRCm39) probably benign Het
Ripk2 T A 4: 16,155,192 (GRCm39) probably null Het
Rpgrip1 T A 14: 52,378,148 (GRCm39) C499S possibly damaging Het
Scarf1 T C 11: 75,414,870 (GRCm39) S515P probably damaging Het
Sgip1 T C 4: 102,772,256 (GRCm39) V215A probably benign Het
Sis T C 3: 72,796,343 (GRCm39) I1813V possibly damaging Het
Slc17a3 A T 13: 24,040,724 (GRCm39) T317S probably benign Het
Slc35e1 T C 8: 73,237,821 (GRCm39) N340S probably benign Het
Smg6 A G 11: 74,820,256 (GRCm39) I176V probably benign Het
Smim17 T C 7: 6,432,325 (GRCm39) L89S probably damaging Het
Synm T C 7: 67,386,051 (GRCm39) N95S probably damaging Het
Tdrd9 A G 12: 112,002,873 (GRCm39) K841E possibly damaging Het
Tep1 G T 14: 51,092,024 (GRCm39) F570L possibly damaging Het
Tgm3 G A 2: 129,868,734 (GRCm39) probably null Het
Tra2b T C 16: 22,071,496 (GRCm39) Y128C possibly damaging Het
Vmn2r17 T C 5: 109,576,110 (GRCm39) V327A probably benign Het
Wdr20rt A T 12: 65,274,088 (GRCm39) D344V probably damaging Het
Zfp940 A G 7: 29,544,363 (GRCm39) C515R probably damaging Het
Other mutations in Rfx4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00094:Rfx4 APN 10 84,676,063 (GRCm39) missense probably damaging 1.00
IGL00334:Rfx4 APN 10 84,615,917 (GRCm39) missense possibly damaging 0.91
IGL00928:Rfx4 APN 10 84,675,978 (GRCm39) missense probably benign 0.04
IGL01063:Rfx4 APN 10 84,704,246 (GRCm39) missense possibly damaging 0.90
IGL01490:Rfx4 APN 10 84,676,715 (GRCm39) missense possibly damaging 0.85
IGL02390:Rfx4 APN 10 84,676,014 (GRCm39) missense probably damaging 1.00
IGL02454:Rfx4 APN 10 84,675,970 (GRCm39) missense possibly damaging 0.83
R0099:Rfx4 UTSW 10 84,730,168 (GRCm39) missense probably benign
R0503:Rfx4 UTSW 10 84,730,196 (GRCm39) missense possibly damaging 0.56
R0924:Rfx4 UTSW 10 84,704,291 (GRCm39) missense probably damaging 1.00
R0930:Rfx4 UTSW 10 84,704,291 (GRCm39) missense probably damaging 1.00
R1386:Rfx4 UTSW 10 84,699,149 (GRCm39) missense probably damaging 1.00
R1738:Rfx4 UTSW 10 84,716,839 (GRCm39) critical splice donor site probably null
R1987:Rfx4 UTSW 10 84,731,952 (GRCm39) missense possibly damaging 0.87
R3717:Rfx4 UTSW 10 84,716,088 (GRCm39) missense probably damaging 1.00
R4231:Rfx4 UTSW 10 84,650,558 (GRCm39) missense probably benign 0.03
R4300:Rfx4 UTSW 10 84,740,966 (GRCm39) missense probably damaging 0.98
R4581:Rfx4 UTSW 10 84,680,164 (GRCm39) missense possibly damaging 0.93
R4582:Rfx4 UTSW 10 84,680,164 (GRCm39) missense possibly damaging 0.93
R4618:Rfx4 UTSW 10 84,716,760 (GRCm39) missense probably benign 0.01
R5156:Rfx4 UTSW 10 84,704,218 (GRCm39) missense probably damaging 1.00
R5185:Rfx4 UTSW 10 84,699,114 (GRCm39) missense probably damaging 1.00
R5377:Rfx4 UTSW 10 84,696,406 (GRCm39) missense possibly damaging 0.81
R5601:Rfx4 UTSW 10 84,634,442 (GRCm39) missense probably damaging 1.00
R5879:Rfx4 UTSW 10 84,650,625 (GRCm39) critical splice donor site probably null
R5996:Rfx4 UTSW 10 84,675,881 (GRCm39) nonsense probably null
R6358:Rfx4 UTSW 10 84,680,099 (GRCm39) missense probably damaging 1.00
R6805:Rfx4 UTSW 10 84,676,092 (GRCm39) missense possibly damaging 0.86
R7248:Rfx4 UTSW 10 84,740,919 (GRCm39) missense probably benign 0.05
R7427:Rfx4 UTSW 10 84,731,876 (GRCm39) missense probably benign 0.28
R7428:Rfx4 UTSW 10 84,731,876 (GRCm39) missense probably benign 0.28
R7514:Rfx4 UTSW 10 84,716,090 (GRCm39) missense probably damaging 1.00
R7576:Rfx4 UTSW 10 84,699,213 (GRCm39) missense probably damaging 0.98
R8002:Rfx4 UTSW 10 84,676,721 (GRCm39) missense probably damaging 0.97
R8838:Rfx4 UTSW 10 84,676,758 (GRCm39) missense probably damaging 1.00
R8938:Rfx4 UTSW 10 84,675,936 (GRCm39) missense probably damaging 1.00
R9359:Rfx4 UTSW 10 84,740,921 (GRCm39) missense probably benign 0.00
R9513:Rfx4 UTSW 10 84,674,050 (GRCm39) start codon destroyed probably null 0.01
RF010:Rfx4 UTSW 10 84,694,351 (GRCm39) critical splice acceptor site probably benign
RF014:Rfx4 UTSW 10 84,694,353 (GRCm39) critical splice acceptor site probably benign
RF015:Rfx4 UTSW 10 84,694,353 (GRCm39) critical splice acceptor site probably benign
RF023:Rfx4 UTSW 10 84,694,349 (GRCm39) critical splice acceptor site probably benign
RF030:Rfx4 UTSW 10 84,694,344 (GRCm39) critical splice acceptor site probably benign
RF035:Rfx4 UTSW 10 84,694,344 (GRCm39) critical splice acceptor site probably benign
RF046:Rfx4 UTSW 10 84,694,345 (GRCm39) critical splice acceptor site probably benign
RF060:Rfx4 UTSW 10 84,694,358 (GRCm39) critical splice acceptor site probably benign
RF062:Rfx4 UTSW 10 84,694,345 (GRCm39) critical splice acceptor site probably benign
X0024:Rfx4 UTSW 10 84,615,938 (GRCm39) missense possibly damaging 0.82
Z1177:Rfx4 UTSW 10 84,731,955 (GRCm39) missense probably benign 0.30
Z1177:Rfx4 UTSW 10 84,650,548 (GRCm39) missense possibly damaging 0.85
Predicted Primers PCR Primer
(F):5'- TTAACTCAGCTCACAGCGAGCAGG -3'
(R):5'- CCTAGTGACACATGAACAGCACGAG -3'

Sequencing Primer
(F):5'- TGGGCACAAGTCCCACAG -3'
(R):5'- CCCTACCTTGGGAAGTTGGAATC -3'
Posted On 2014-05-14